Matt Shirley
22 May 2013
Mikhail Gorbachev, president of former USSR
(A,B) Photographs of a subject with the Sturge–Weber syndrome. (C) PWS from subject without SWS. (D,E,F) Brain MRI from subject with SWS. Arrows: white - atrophy, yellow - leptomeninges, red - choroid. Shirley et al. 2013 NEJM
For somatic mutation detection from paired samples we use Strelka1.
| Subject | Somatic SNVs | Tissue |
|---|---|---|
| 1 | 325 | PWS |
| 2 | 543 | Brain |
| 3 | 427 | PWS |
Variants in → disease alleles out
1294 variants → 1 candidate variant: GNAQ R183Q
Blue box: variants having a mutant allele in affected sample and not in normal tissue samples
M = sum of log transformed allele frequencies
A = difference of log transformed allele frequencies
GNAQ is still the only shared coding somatic variant
Image from EuroEPINOMICS3
in fixed checksum
CATAACT CAAAACT A > T at pos 3
AGAGAGA AGAGAGA ok
TCACAGC TCACAGC ok
GAACAGG GAAAAGG A > C at pos 4
CTATAGT CTATAGT ok
TTTAAAN NNNNNNN bad
NNNNNNN NNNNNNN bad
Based on this simulation, we targeted > 10,000 and achieved 2446 to 93,008 (median, 12,947) read depth.
| # Subjects | Tissue | SWS | GNAQ R183Q | Detection method |
|---|---|---|---|---|
| 9 | PWS | Yes | 100% | Amplicon seq |
| 7 | Skin | Yes | 14% | Amplicon seq |
| 13 | PWS | No | 92% | Amplicon seq, Primer extension |
| 18 | Brain | Yes | 88% | Amplicon seq |
| 6 | Brain | No | 0% | Amplicon seq |
| 4 | Brain | CCM | 0% | Primer extension |
| 669 | Blood/LCL | N/A | 0.7% | Exome seq |
CCM = cerebral cavernous malformation
Amplicon seq = 12,947X median read depth
Exome seq = 271X median read depth
Primer extension = SNaPshot allele-specific primer extension
Closed circle: Mutant GNAQ alone, Open circle: Mutant GNAQ plus RGS4
Berman 1996 Cell
Two arms of the MAPK pathway
Vaqué 2012 Molecular Cell
Dr. Garry Cutting
Dr. Dani Fallin
Dr. Sarah Wheelan
Dr. Ingo Ruczinski
Dr. Anne Comi (Kennedy Krieger Institute)
Dr. Douglas Marchuk (Duke University)
Dr. Bernard Cohen (Kennedy Krieger Institute)
Dr. Paula North (Medical College of Wisconsin)
Dr. Hao Tang (Duke University)
Carol Gallione (Duke University)
Patients and families
BCMB program at Hopkins
Dr. Carolyn Machamer
Margie Policastri
Sharon Root
Dr. Leslie Brown
Dr. Arhonda Gogos
Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., & Cheetham, R. K. (2012). Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics.↩
Yandell, M., Huff, C., Hu, H., Singleton, M., Moore, B., Xing, J., et al. (2011). A probabilistic disease-gene finder for personal genomes. Genome Research, 21(9), 1529–1542. doi:10.1101/gr.123158.111↩
http://158.64.76.154/euroepinomicsblog/post/1640-sturge-weber-syndrome-explained-somatic-mutations-in-gnaq↩
Lee, C.-W., Choi, D.-Y., Oh, Y.-G., Yoon, H.-S., & Kim, J.-D. (2005). An infantile case of Sturge-Weber syndrome in association with Klippel-Trenaunay-Weber syndrome and phakomatosis pigmentovascularis. Journal of Korean medical science↩
Robaee, Al, A., Banka, N., & Alfadley, A. (2004). Phakomatosis pigmentovascularis type IIb associated with Sturge-Weber syndrome. Pediatric Dermatology↩
Bystrykh, L. V. (2012). Generalized DNA Barcode Desig Based on Hamming Codes. (J.-A. L. Stanton, Ed.)PLoS ONE.↩
Berman, D. M., Wilkie, T. M., & Gilman, A. G. (1996). GAIP and RGS4 Are GTPase-Activating Proteins for the G Subfamily of G Protein ? Subunits. Cell.↩
Vaqué, J. P., Dorsam, R. T., Feng, X., Iglesias-Bartolome, R., Forsthoefel, D. J., Chen, Q., et al. (2012). A Genome-wide RNAi Screen Reveals a Trio-Regulated Rho GTPase Circuitry Transducing Mitogenic Signals Initiated by G Protein-Coupled Receptors. Molecular Cell↩